th_PulseChase: Analytical solution to stem cell label drift model....

In MorrisseyLab/CryptDriftR: Analyse crypt lineage tracing data

Description

Analytical solution to stem cell label drift model. th_PulseChase Stochastic model used in "Defining stem cell dynamics in models of intestinal tumor initiation." Vermeulen, Morrissey, et. al. Science 2013. The model is a stochastic birth death model with absorbing boundaries at 0 and N.

Usage

th_PulseChase(
  lambda,
  Ns,
  tau,
  time_points,
  persisting = T,
  Pr = 0.5,
  splitNum = 0,
  alpha_beta = NULL
)

Arguments

lambda	Stem cell replacement rate.
Ns	Number of functional stem cells per crypt.
tau	Time delay until drift starts.
time_points	vector of time point values.
persisting	Whether or not to return probability distribution of only the surviving clones or not.
Pr	Bias in stem cell replacement Pr = 0.5 is neutral.
splitNum	To match to data choose the number of bins to distribute the model into (e.g 1/8s, splitNum = 8).
alpha_beta	two dim vector giving rate of replacement, alternative to using Pr. The relation is beta = 2*lambda*Pr, alpha = 2*lambda*(1-Pr)

Value

a matrix with the solution to the neutral or biased drift model.

Examples

x = th_PulseChase(lambda = 0.1, Ns = 5, tau = 1, time_points = 1:50)

MorrisseyLab/CryptDriftR documentation built on Aug. 7, 2021, 8:22 p.m.